Human immunodeficiency virus type 1 (HIV-1) infects predominantly CD4+ cells in human peripheral blood and infection is associated with CD4+ lymphocyte dysfunction in patients with AIDS. To determine the frequency of HIV-1 infection in CD4+ lymphocytes in vivo, peripheral blood CD4+ lymphocytes were isolated by fluorescence-activated cell sorting from HIV-1-infected persons with clinical disease ranging from asymptomatic to AIDS. Using standard and booster polymerase chain reaction analyses, study patients with AIDS and AIDS-related complex (ARC) were found to harbor the HIV-1 genome in at least 10% of CD4+ lymphocytes, and approximately 10-fold less infected cells were found in those with asymptomatic infection. In addition, the peripheral blood mononuclear cells from patients with ARC frequently contained a higher absolute number of HIV-1-infected CD4+ lymphocytes than those with AIDS or asymptomatic infection. It is likely that this high level of infection of CD4+ lymphocytes is the primary cause for the progressive immunologic deficiency observed in patients infected with HIV-1.